数据与复现生物信息与基因组学FreedomIntelligence/OpenClaw-Medical-Skills数据与复现

bio-chipseq-motif-analysis

维护者 FreedomIntelligence · 最近更新 2026年4月1日

De novo motif discovery and known motif enrichment analysis using HOMER and MEME-ChIP. Identify transcription factor binding motifs in ChIP-seq, ATAC-seq, or other genomic peak data. Use when finding enriched DNA motifs in peak sequences.

OpenClawNanoClaw分析处理复现实验bio-chipseq-motif-analysis🧬 bioinformatics (gptomics bio-* suite)bioinformatics — epigenomics & chromatinde

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-chipseq-motif-analysis

维护者: FreedomIntelligence
许可: MIT
最近更新: 2026年4月1日

技能摘要

来自 SKILL.md 的关键信息

2 min

核心说明

CLI：findMotifsGenome.pl peaks.bed hg38 output/ (HOMER)，meme-chip -db JASPAR peaks.fa (MEME)。
Find enriched motifs in my ChIP-seq peaks" → Discover de novo DNA-binding motifs 、 test ，用于 known TF motif enrichment in peak sequences. CLI：findMotifsGenome.pl peaks.bed hg38 output/ (HOMER)，meme-chip -db JASPAR peaks.fa (MEME)。
Identify DNA sequence motifs enriched in ChIP-seq 或 ATAC-seq peaks to discover transcription factor binding sites。
perl /path/to/homer/configureHomer.pl -install hg38 perl /path/to/homer/configureHomer.pl -install mm10。

原始文档

SKILL.md 摘录

Tool Comparison

Tool	Strengths	Use Case
HOMER	Fast, comprehensive, built-in databases	General motif analysis
MEME-ChIP	Multiple algorithms, web interface	Publication-quality
MEME	De novo discovery only	Simple discovery
FIMO	Known motif scanning	Genome-wide scanning

Installation

conda install -c bioconda homer

## De Novo Motif Discovery

**Goal:** Discover enriched DNA-binding motifs directly from ChIP-seq peak sequences.

**Approach:** Run findMotifsGenome.pl on a peak BED file with a specified fragment size, optionally providing background regions and target motif lengths.

```bash